PDBsum entry 2a9g

Hydrolase

PDB id: 2a9g

Contents

Protein chains

405 a.a. *

Ligands

ARG ×4

Waters ×1064

* Residue conservation analysis

PDB id:

2a9g

Name:

Hydrolase

Title:

Structure of c406a arginine deiminase in complex with l-arginine

Structure:

Arginine deiminase. Chain: a, b, c, d. Synonym: adi, arginine dihydrolase, ad. Engineered: yes. Mutation: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: arca. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.30Å R-factor: 0.199 R-free: 0.267

Authors:

A.Galkin,X.Lu,D.Dunaway-Mariano,O.Herzberg

Key ref:

A.Galkin et al. (2005). Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase. J Biol Chem, 280, 34080-34087. PubMed id: 16091358 DOI: 10.1074/jbc.M505471200

Date:

11-Jul-05 Release date: 09-Aug-05

Protein chains

P13981  (ARCA_PSEAE) -  Arginine deiminase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 418 a.a.

Struc: 405 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.5.3.6 - arginine deiminase.
• Reaction: L-arginine + H2O = L-citrulline + NH4⁺

L-arginine + H2O (Bound ligand (Het Group name = ARG) corresponds exactly) = L-citrulline + NH4(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M505471200

J Biol Chem 280:34080-34087 (2005)

PubMed id: 16091358

Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase.

A.Galkin, X.Lu, D.Dunaway-Mariano, O.Herzberg.

ABSTRACT

L-arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In this study, the structure of the C406A mutant in complex with L-arginine is reported to provide a snapshot of the enzyme.substrate complex. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers. His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S-alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.

Selected figure(s)

Figure 1.
FIGURE 1. The reactions catalyzed by ADI superfamily members. A, ADI; B, DDAH; C, PAD; D, arginine:glycine amidinotransferase (AGAT); E, arginine:inosamine-phosphate amidinotransferase (IPAT).

Figure 5.
FIGURE 5. A feasible mechanism of PaADI catalysis of L-arginine hydrolysis to citrulline and ammonia.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 34080-34087) copyright 2005.

Figures were selected by an automated process.